nf-core/drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Global parameters for the pipeline.
Path to the samplesheet file used by the pipeline. The file should be a TSV file. Equivalent to the sampleAnnotation parameter in the snakemake pipeline.
string^\S+\.tsv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. Equivalent to the root parameter in the snakemake pipeline.
stringMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringTitle of the project to be displayed on the rendered HTML output
stringEquivalent to the genomeAssembly parameter in the snakemake pipeline. Either hg19/hs37d5 or hg38/GRCh38, depending on the genome assembly used for mapping
stringPath to GTF gene annotations file. Equivalent to the geneAnnotation parameter in the snakemake pipeline, with the difference that a file depicting the kev-value pairs is expected here instead.
string^\S+\.(csv|tsv|json|yml|yaml)$Full path of the file containing HPO terms. If missing, it reads it from our webserver. Refer to files-to-download. Equivalent to the hpoFile parameter in the snakemake pipeline.
string^\S+\.tsv(\.gz)?$Specify a random seed for reproducibility
boolean,integerExport counts options.
A comma-separated list of gene annotations to export.
stringA comma-separated list of aberrant expression and aberrant splicing groups whose counts should not be exported. If empty, all groups are exported.
stringAberrant expression options.
Skip aberrant expression analysis.
booleanA comma-separated list of aberrant expression groups to run. If empty, all groups are run.
stringA positive number indicating the minimum number of samples that a group needs in order to be analyzed. We recommend at least 50.
integer1A positive number indicating the minimum FPKM value for a gene to be considered expressed.
integer1Methods to remove sample covariation in OUTRIDER.
stringA number between (0, 1] indicating the maximum FDR an event can have in order to be considered an outlier.
number0.05A non-negative number. Z scores (in absolute value) greater than this cutoff are considered as outliers.
numberAn integer that controls the maximum value that the encoding dimension can take.
integer3An integer that sets the batch size for counting reads within a bam file. If memory issues persist lower the yieldSize.
integer2000000Full path to a yaml file specifying lists of candidate genes per sample to test during FDR correction. See the documentation for details on the structure of this file.
string^\S+\.(yaml|yml)$Aberrant splicing options.
Skip aberrant splicing analysis.
booleanA comma-separated list of aberrant splicing groups to run. If empty, all groups are run.
stringA positive number indicating the minimum number of samples that a group needs in order to be analyzed. We recommend at least 50.
integer1If true, it forces samples to be recounted.
booleanSet to true only if counting Nanopore or PacBio long reads.
booleanSet to true if non standard chromosomes are to be kept for further analysis.
booleanIf true, no filter is applied. We recommend filtering.
booleanThe minimal read count in at least one sample required for an intron to pass the filter.
integer20The minimum total read count (N) an intron needs to have at the specified quantile across samples to pass the filter. See —as_quantile_for_filtering.
integer10The minimal variation (in delta psi) required for an intron to pass the filter.
number0.05Methods to remove sample covariation in FRASER.
stringVersion of FRASER to use.
stringFRASERA non-negative number. Delta psi values greater than this cutoff are considered as outliers. Recommand 0.3 for FRASER, 0.1 for FRASER2.
number0.3Defines at which percentile the as_quantile_min_expression filter is applied. Recommand 0.95 for FRASER, 0.75 for FRASER2.
number0.95Same as in aberrant expression.
number0.1An integer that controls the maximum value that the encoding dimension can take.
integer6Full path to a yaml file specifying lists of candidate genes per sample to test during FDR correction. See the documentation for details on the structure of this file.
string^\S+\.(yaml|yml)$Mono-allelic expression options.
Skip mono-allelic expression analysis.
booleanA comma-separated list of mono-allelic expression groups to run. If empty, all groups are run.
stringPath to UCSC FASTA genome file. Equivalent to the ucsc option in the genome parameter in the snakemake pipeline.
string^\S+\.fn?a(sta)?(\.gz)?$Path to UCSC FASTA index file.
string^\S+\.fai$Path to UCSC sequence dictionary file. . If not provided, the pipeline will try to create it from the FASTA file.
string^\S+\.dict$Path to NCBI FASTA genome file. Equivalent to the ncbi option in the genome parameter in the snakemake pipeline.
string^\S+\.fn?a(sta)?(\.gz)?$Path to NCBI FASTA index file.
string^\S+\.fai$Path to NCBI sequence dictionary file. If not provided, the pipeline will try to create it from the FASTA file.
string^\S+\.dict$If true (recommended), it emits the header warnings of a VCF file when performing the allelic counts
booleanSame as in aberrant expression.
number0.05A number between [0.5, 1) indicating the maximum allelic ratio allele1/(allele1+allele2) for the test to be significant.
number0.8Add the allele frequencies from gnomAD
booleanMaximum allele frequency (of the minor allele) cut-off. Variants with AF equal or below this number are considered rare.
number0.001Maximum variant frequency among the cohort.
number0.05Full path to the vcf file used for VCF-BAM matching. Refer to files-to-download.
string^\S+\.vcf\.gz$Full path to the index of the vcf file used for VCF-BAM matching. Refer to files-to-download
string^\S+\.tbi$Same as ‘groups’, but for the VCF-BAM matching
stringfraction (0-1) used to seperate ‘matching’ samples and ‘non-matching’ samples comparing the DNA and RNA data during QC.
number0.05Reference genome related files and options required for the workflow.
Do not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/drop/data/Base URL or local path to location of module test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string